Neisseria gonorrhoeae is the causative agent of the sexually transmitted disease (STD) gonorrhea, a high morbidity disease worldwide with an estimated 62 million cases annually (WHO). Although infection of the male urethra is usually symptomatic, nearly 80% of females infected with N. gonorrhoeae are asymptomatic. This is particularly dangerous as prolonged untreated gonococcal infections can lead to pelvic inflammatory disease (PID), a common cause of infertility and ectopic pregnancy. Through an existing Clinical Core in partnership with a NIAID funded U19 grant (AI084048), we have the unique opportunity to work with our collaborators at the National Center for STD Control (NCSTD) in Nanjing, China to address the disparity in symptomatic responses to N. gonorrhoeae infection. The NCSTD clinic currently obtains urethral specimens from males who report with gonococcal symptoms. These men are often co-infected with one or more STIs. The NCSTD also obtains matched cervico-vaginal lavage specimens from females who may be infected with gonococcal or gonococcal/chlamydial strains contracted from their matched male partners. We propose in this study to use RNA deep sequencing to define genital mucosal responses to gonorrhea, how they shift during gonococcal infection, and how differential male and female responses lead to different symptomatic outcomes in both. In new studies we have utilized RNA seq analysis to define the global transcriptome of N. gonorrhoeae during in vivo infection and during in vitro incubation with host cells. Our analysis revealed a unique signature of gonococcal stress response, metabolism, and respiratory genes expressed during in vivo infection. Based on these results we hypothesize N. gonorrhoeae expresses a unique set of genes during in vivo infection that is influenced by the specific host environment present during infection of the male and female genital tract. Furthermore, host gender-specific differences result in distinct gonococcal transcriptomes. We propose the following Aims to address this hypothesis: Aim 1. To compare the transcriptomic profile of N. gonorrhoeae during in vivo infection of the female genital tract to incubation with endocervical epithelial cells and growth i vitro in media. Aim 2. To compare the transcriptomic profile of N. gonorrhoeae during in vivo infection of the male genital tract to incubation with urethral epithelial cells and growth in vitr in media. Aim 3. To compare the transcriptomic profile of N. gonorrhoeae during in vivo infection of both male and female genital tract and incubation with male urethral epithelial cells and endocervical epithelial cells.